Create VAF corplots of tumors across multiple timepoints for thr autopsy samples in the PBTA Cohort

Tumor evolution project

Data used

In this notebook, we are using the maf_autopsy.tsv file generated from the 01-preprocess-data.Rmd script. We will also use the oncoprint goi list from OpenPedCan oncoprint-goi-lists-OpenPedCan-gencode-v39.csv.

Set up

suppressPackageStartupMessages({
  library(tidyverse)
  library(ggrepel)
})

Directories and File Inputs/Outputs

# Detect the ".git" folder. This will be in the project root directory.
# Use this as the root directory to ensure proper sourcing of functions
# no matter where this is called from.
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
scratch_dir <- file.path(root_dir, "scratch")
analysis_dir <- file.path(root_dir, "analyses", "tmb-vaf-longitudinal") 
input_dir <- file.path(analysis_dir, "input")

# Input files
maf_autopsy_file <- file.path(scratch_dir, "maf_autopsy.tsv")
oncoprint_goi_file <- file.path(input_dir, "oncoprint-goi-lists-OpenPedCan-gencode-v39.csv")
palette_file <- file.path(root_dir, "figures", "palettes", "timepoint_color_palette.tsv")

# File path to plots directory
plots_dir <-
  file.path(analysis_dir, "plots")
if (!dir.exists(plots_dir)) {
  dir.create(plots_dir)
}

# File path to results directory
results_dir <-
  file.path(analysis_dir, "results")
if (!dir.exists(results_dir )) {
  dir.create(results_dir)
}

source(paste0(analysis_dir, "/util/function-create-corplot.R"))
source(paste0(root_dir, "/figures/scripts/theme.R"))

Read in data and process

# Read maf_autopsy file generated from step `01-process-data.Rmd`
maf_autopsy_raw <- readr::read_tsv(maf_autopsy_file, guess_max = 100000, show_col_types = FALSE) %>% 
  group_by(Kids_First_Participant_ID) %>% 
  mutate(cg_distinct = n_distinct(cancer_group) > 1 # to identify samples with different diagnosis across timepoints
         ) 

# So far we have one PT_1H2REHT2 patient case with a secondary diagnosis in one of the progressive samples
# To reflect this kind of situation we create cg_sum column
maf_autopsy <- maf_autopsy_raw %>% 
  distinct(cancer_group, .keep_all = TRUE) %>% 
  summarise(cg_sum = str_c(cancer_group, collapse=",")) %>%
  left_join(maf_autopsy_raw, by = c("Kids_First_Participant_ID"))

# Read oncoprint_goi_file
# We will use the following list of genes and then we will create a label to select the ones for the corplots.
oncoprint_goi <- read.csv(oncoprint_goi_file, stringsAsFactor = FALSE) %>%
  select(LGAT, Embryonal.tumor, HGAT, Other) 

# let's create a list with the genes to be used for the corplots
oncoprint_goi <- data.frame(goi_list = unlist(oncoprint_goi)) 

# remove empty rows
oncoprint_goi <- oncoprint_goi[!apply(oncoprint_goi == "", 1, all), ] 
oncoprint_goi <- data.frame(oncoprint_goi)

# Read palette_df file
palette_df <- readr::read_tsv(palette_file, guess_max = 100000, show_col_types = FALSE)

Corplots for each Patient case and per biospecimen_id and timepoint

# Save results by cg_sum
cg_names <- unique(as.character(maf_autopsy$cg_sum))
print(cg_names)

[1] "Diffuse midline glioma"             "High-grade glioma,Low-grade glioma" "Medulloblastoma"                   
[4] "High-grade glioma"                  "Atypical Teratoid Rhabdoid Tumor"   "Chordoma"                          
[7] "Ependymoma"                         "Ewing sarcoma"                      "Adamantinomatous Craniopharyngioma"

# Loop through cg_sum
for (x in 1:length(cg_names)){
  print(x)
  
  cg_maf_sub <- maf_autopsy %>%
    filter(cg_sum == cg_names[x])
 
    # We will define samples based on the "Kids_First_Participant_ID" column 
    samples <- unique(as.character(cg_maf_sub$Kids_First_Participant_ID))
    print(samples)
    
    # define cg_sum specific plots dir
    cg_plots_dir <- file.path(plots_dir, cg_names[x])
    if (!dir.exists(cg_plots_dir)) {
      dir.create(cg_plots_dir)
    }
    
    # define cg_sum specific results dir
    cg_results_dir <- file.path(results_dir, cg_names[x])
    if (!dir.exists(cg_results_dir)) {
      dir.create(cg_results_dir)
      }
  
    # Run loop for each sample and pair
    for (i in seq_along(samples)) {
  print(i)
  maf_sub <- cg_maf_sub %>%
    filter(Kids_First_Participant_ID == samples[i])
  timepoints_other_plots <- unique(maf_sub$timepoints_other)
  timepoints_other_plots <- timepoints_other_plots[!timepoints_other_plots == "4"]
  print(timepoints_other_plots)
  timepoints_deceased_plots <- unique(maf_sub$timepoints_deceased)
  timepoints_deceased_plots <- timepoints_deceased_plots[!timepoints_deceased_plots %in% c("1", "2", "3")]
  print(timepoints_deceased_plots)
  
 #  for (y in 1:length(maf_sub$cg_sum)){
 #   if (maf_sub$cg_sum[y] == "FALSE"){
  #   print ("Single diagnosis across timepoints")
  #    } else {
   #     print ("Multiple diagnosis across timepoints")
   #     next
   #   }

  # Run corplot function
  for (t in seq_along(timepoints_deceased_plots)){
    for (k in seq_along(timepoints_other_plots)){
      fname <- paste0(cg_plots_dir, "/", samples[i], "-", timepoints_other_plots[k], "-vs-", timepoints_deceased_plots[t], "-vaf-corplot.pdf")
      print(fname)
      p <- create_corplot(maf = maf_sub,
                          timepoints_other_plot = timepoints_other_plots[k],
                          timepoints_deceased_plot = timepoints_deceased_plots[t],
                          sid = samples[i])
      pdf(file = fname, width = 10, height = 8)
      print(p)
      dev.off()

    }
  }
  }  
    }

[1] 1
[1] "PT_19GCSK2S" "PT_5NS35B66" "PT_FA2F3HQG" "PT_GTHZF21E" "PT_KTRJ8TFY" "PT_KZ56XHJT" "PT_MNSEJCDM" "PT_PR4YBBH3"
[1] 1
[1] "Diagnosis_BS_3KD309X6"
[1] "Deceased_BS_AH252MTC" "Deceased_BS_FZ8D57HJ" "Deceased_BS_GH6PH611" "Deceased_BS_NXT37ZPA"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_AH252MTC-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_FZ8D57HJ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_GH6PH611-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_NXT37ZPA-vaf-corplot.pdf"
[1] 2
[1] "Diagnosis_BS_SVKMG97S"
[1] "Deceased_BS_F0JN3TFM"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_5NS35B66-Diagnosis_BS_SVKMG97S-vs-Deceased_BS_F0JN3TFM-vaf-corplot.pdf"
[1] 3
[1] "Diagnosis_BS_G9WRA2N1"
[1] "Deceased_BS_S78482NX"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_FA2F3HQG-Diagnosis_BS_G9WRA2N1-vs-Deceased_BS_S78482NX-vaf-corplot.pdf"
[1] 4
[1] "Diagnosis_BS_N4S9T8F5"
[1] "Deceased_BS_3A7YMV93" "Deceased_BS_5PR4KXE1" "Deceased_BS_D3BH8D4Y" "Deceased_BS_EV071CE1" "Deceased_BS_FQBVBTCY" "Deceased_BS_M4KR9DSE"
[7] "Deceased_BS_T3WNX1E2" "Deceased_BS_Z7806Z75"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_3A7YMV93-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_5PR4KXE1-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_D3BH8D4Y-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_EV071CE1-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_FQBVBTCY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_M4KR9DSE-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_T3WNX1E2-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_Z7806Z75-vaf-corplot.pdf"
[1] 5
[1] "Diagnosis_BS_3VKW5988" "Diagnosis_BS_402W79TS" "Diagnosis_BS_BQ81D2BP"
[1] "Deceased_BS_5968GBGT" "Deceased_BS_AF5D41PD" "Deceased_BS_EE73VE7V" "Deceased_BS_HYKV2TH9"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"
[1] 6
[1] "Progressive_BS_0ATJ22QA" "Progressive_BS_9DN4QR6E" "Diagnosis_BS_FWP8ZA4K"   "Diagnosis_BS_H8NWA41N"  
[1] "Deceased_BS_1Q524P3B" "Deceased_BS_22VCR7DF" "Deceased_BS_AK9BV52G" "Deceased_BS_D6STCMQS" "Deceased_BS_X5VN0FW0" "Deceased_BS_YHXMYDBN"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
[1] 7
[1] "Diagnosis_BS_CBMAWSAR" "Diagnosis_BS_ZSH09N84"
[1] "Deceased_BS_J8EH1N7V" "Deceased_BS_Y74XAFJX"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_CBMAWSAR-vs-Deceased_BS_J8EH1N7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_ZSH09N84-vs-Deceased_BS_J8EH1N7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_CBMAWSAR-vs-Deceased_BS_Y74XAFJX-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_ZSH09N84-vs-Deceased_BS_Y74XAFJX-vaf-corplot.pdf"
[1] 8
[1] "Diagnosis_BS_PPY0EWPG"
[1] "Deceased_BS_C2NH5FDT"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_PR4YBBH3-Diagnosis_BS_PPY0EWPG-vs-Deceased_BS_C2NH5FDT-vaf-corplot.pdf"
[1] 2
[1] "PT_1H2REHT2"
[1] 1
[1] "Progressive_BS_79SYEHY3" "Progressive_BS_7M7JNG00"
[1] "Deceased_BS_96S0VQBN"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma,Low-grade glioma/PT_1H2REHT2-Progressive_BS_79SYEHY3-vs-Deceased_BS_96S0VQBN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma,Low-grade glioma/PT_1H2REHT2-Progressive_BS_7M7JNG00-vs-Deceased_BS_96S0VQBN-vaf-corplot.pdf"
[1] 3
[1] "PT_23NZGSRJ" "PT_CXT81GRM" "PT_NZ85YSJ1"
[1] 1
[1] "Diagnosis_BS_05S9WJW6"
[1] "Deceased_BS_209RV8H2" "Deceased_BS_CCHHH752" "Deceased_BS_CJ2G78ZZ" "Deceased_BS_F2MTFYFR" "Deceased_BS_GNXGGWFN" "Deceased_BS_H8JZ6CZR"
[7] "Deceased_BS_Q03MVGN6"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_209RV8H2-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_CCHHH752-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_CJ2G78ZZ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_F2MTFYFR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_GNXGGWFN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_H8JZ6CZR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_Q03MVGN6-vaf-corplot.pdf"
[1] 2
[1] "Diagnosis_BS_HZNKSQ17"
[1] "Deceased_BS_3CG2N4PD"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_CXT81GRM-Diagnosis_BS_HZNKSQ17-vs-Deceased_BS_3CG2N4PD-vaf-corplot.pdf"
[1] 3
[1] "Diagnosis_BS_4HRYS7JY"
[1] "Deceased_BS_Q7QH96SX"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_NZ85YSJ1-Diagnosis_BS_4HRYS7JY-vs-Deceased_BS_Q7QH96SX-vaf-corplot.pdf"
[1] 4
[1] "PT_37B5JRP1" "PT_394ZA6P7" "PT_3CHB9PK5" "PT_8GN3TQRM" "PT_KBFM551M" "PT_MDWPRDBT" "PT_Z4BF2NSB"
[1] 1
[1] "Diagnosis_BS_EJV0N3BX"
[1] "Deceased_BS_8Q8N6AHW"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_37B5JRP1-Diagnosis_BS_EJV0N3BX-vs-Deceased_BS_8Q8N6AHW-vaf-corplot.pdf"
[1] 2
[1] "Diagnosis_BS_1KP6JADZ"
[1] "Deceased_BS_Q41J76W9"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_394ZA6P7-Diagnosis_BS_1KP6JADZ-vs-Deceased_BS_Q41J76W9-vaf-corplot.pdf"
[1] 3
[1] "Diagnosis_BS_20TBZG09"
[1] "Deceased_BS_8AY2GM4G"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_3CHB9PK5-Diagnosis_BS_20TBZG09-vs-Deceased_BS_8AY2GM4G-vaf-corplot.pdf"
[1] 4
[1] "Recurrence_BS_QQP17PDQ"  "Progressive_BS_RXSBJ929"
[1] "Deceased_BS_S791VC80"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_8GN3TQRM-Recurrence_BS_QQP17PDQ-vs-Deceased_BS_S791VC80-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_8GN3TQRM-Progressive_BS_RXSBJ929-vs-Deceased_BS_S791VC80-vaf-corplot.pdf"
[1] 5
[1] "Diagnosis_BS_9P4NDTKJ" "Diagnosis_BS_M0B42FPR" "Diagnosis_BS_M5FM63EB" "Diagnosis_BS_WYTDVC0Y"
[1] "Deceased_BS_J8EK6RNF"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_9P4NDTKJ-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_M0B42FPR-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_M5FM63EB-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_WYTDVC0Y-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
[1] 6
[1] "Recurrence_BS_00TRPEQX"  "Recurrence_BS_BQWMQM2Y"  "Progressive_BS_D368BNRD"
[1] "Deceased_BS_1M63B97V"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_MDWPRDBT-Recurrence_BS_00TRPEQX-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_MDWPRDBT-Recurrence_BS_BQWMQM2Y-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_MDWPRDBT-Progressive_BS_D368BNRD-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"
[1] 7
[1] "Recurrence_BS_EJP43CD9" "Diagnosis_BS_W2QCHQ7E" 
[1] "Deceased_BS_2T4EJ6KN" "Deceased_BS_537YFJ06" "Deceased_BS_C6T8F9K7" "Deceased_BS_GSXNQNRY" "Deceased_BS_M29BNE7Z" "Deceased_BS_MRN9VDQ0"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_2T4EJ6KN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_2T4EJ6KN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_537YFJ06-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_537YFJ06-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_C6T8F9K7-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_C6T8F9K7-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_GSXNQNRY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_GSXNQNRY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_M29BNE7Z-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_M29BNE7Z-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_MRN9VDQ0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_MRN9VDQ0-vaf-corplot.pdf"
[1] 5
[1] "PT_3KM9W8S8" "PT_6N825561" "PT_DVXE38EX" "PT_RJ1TJ2KH"
[1] 1
[1] "Diagnosis_BS_859AV1DB"
[1] "Deceased_BS_2NQXY528" "Deceased_BS_4BB136DY" "Deceased_BS_EQQZ90JQ" "Deceased_BS_MS8TBCWJ" "Deceased_BS_P8FXRTZ2" "Deceased_BS_QR84QJN4"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_2NQXY528-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_4BB136DY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_EQQZ90JQ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_MS8TBCWJ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_P8FXRTZ2-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_QR84QJN4-vaf-corplot.pdf"
[1] 2
[1] "Progressive_BS_E0S2Y0TS"
[1] "Deceased_BS_0YWFFRYV" "Deceased_BS_3V7ZNBTG" "Deceased_BS_YTCYVVY9"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_0YWFFRYV-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_3V7ZNBTG-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_YTCYVVY9-vaf-corplot.pdf"
[1] 3
[1] "Diagnosis_BS_NSWP72M6"   "Progressive_BS_P3R9QZKP" "Recurrence_BS_Y386XSV3" 
[1] "Deceased_BS_ERRA7V0W"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_DVXE38EX-Diagnosis_BS_NSWP72M6-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_DVXE38EX-Progressive_BS_P3R9QZKP-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_DVXE38EX-Recurrence_BS_Y386XSV3-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"
[1] 4
[1] "Diagnosis_BS_6GN1FGTB"
[1] "Deceased_BS_6VKKMM6M"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_RJ1TJ2KH-Diagnosis_BS_6GN1FGTB-vs-Deceased_BS_6VKKMM6M-vaf-corplot.pdf"
[1] 6
[1] "PT_75HRTX4S" "PT_HFQNKP5X"
[1] 1
[1] "Diagnosis_BS_7YGM7F5R"
[1] "Deceased_BS_3CDQYJ5Q" "Deceased_BS_WTGPN218"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_75HRTX4S-Diagnosis_BS_7YGM7F5R-vs-Deceased_BS_3CDQYJ5Q-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_75HRTX4S-Diagnosis_BS_7YGM7F5R-vs-Deceased_BS_WTGPN218-vaf-corplot.pdf"
[1] 2
[1] "Recurrence_BS_6F49F7WH"  "Progressive_BS_9GN1QA3Q" "Progressive_BS_FBJ516WW"
[1] "Deceased_BS_2MPNPD28" "Deceased_BS_5B6XZ7YP" "Deceased_BS_FVPZ3CYY" "Deceased_BS_MAHWW7NR" "Deceased_BS_SCW1FS55" "Deceased_BS_VZB4K7NV"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"
[1] 7
[1] "PT_DNAJYFZT" "PT_NJQ26FHN"
[1] 1
[1] "Recurrence_BS_EJ1H9PZY"
[1] "Deceased_BS_8XJJVBQP"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_DNAJYFZT-Recurrence_BS_EJ1H9PZY-vs-Deceased_BS_8XJJVBQP-vaf-corplot.pdf"
[1] 2
[1] "Recurrence_BS_JZ61AA7Z" "Diagnosis_BS_NXTB7A9N" 
[1] "Deceased_BS_7XEEQM3X" "Deceased_BS_AYR6PJN0"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Recurrence_BS_JZ61AA7Z-vs-Deceased_BS_7XEEQM3X-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Diagnosis_BS_NXTB7A9N-vs-Deceased_BS_7XEEQM3X-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Recurrence_BS_JZ61AA7Z-vs-Deceased_BS_AYR6PJN0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Diagnosis_BS_NXTB7A9N-vs-Deceased_BS_AYR6PJN0-vaf-corplot.pdf"
[1] 8
[1] "PT_HJMP6PH2"
[1] 1
[1] "Recurrence_BS_9SVMVJ45" "Diagnosis_BS_XKM2EAT4" 
[1] "Deceased_BS_3XW15QAZ" "Deceased_BS_4CT3A9PQ" "Deceased_BS_FS48BMA3" "Deceased_BS_GXFX6VW1" "Deceased_BS_RNAADGMF"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_3XW15QAZ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_3XW15QAZ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_4CT3A9PQ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_4CT3A9PQ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_FS48BMA3-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_FS48BMA3-vaf-corplot.pdf"
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#}